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Compared with the traditional method of water quality management, using remote sensing technology in monitoring the water quality has a wider application perspective. For a water body of large scale, the Moderate resolution Imaging Spectroradiometer (MODIS) is more appropriate data for its high temporal resolution for timely and dynamic monitoring, moderate spatial resolution and no charge for acquiring data. In this paper, based on the algorithm of water body extraction and water quality parameters inversion models, and with the lower Yangtze River basin as the study area, we tended to study the comprehensive management of urban water quality using MODIS L1B data. At last, Water quality monitoring information system (WMIS) was proposed, which included three layers: data layer, processing layer and application layer. WMIS provided a new way to monitor the water quality through the integration of remote sensing data and measured data into a system.